rs4771996

Variant names:

• chr13-97401538-G-A
• rs4771996

Your query was ambiguous. Multiple possible variants found:

• chr13-97401538-G-A
• chr13-97401538-G-C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.828 in 152,096 control chromosomes in the GnomAD database, including 52,470 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.83 (52470 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0770
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.828 AC: 125852 AN: 151976 Hom.: 52415 Cov.: 31

Gnomad AFR AF: 0.904

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.804

Gnomad ASJ AF: 0.914

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.824

Gnomad FIN AF: 0.712

Gnomad MID AF: 0.946

Gnomad NFE AF: 0.803

Gnomad OTH AF: 0.843

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.828 AC: 125962 AN: 152096 Hom.: 52470 Cov.: 31 AF XY: 0.825 AC XY: 61329 AN XY: 74342

African (AFR) AF: 0.904 AC: 37536 AN: 41514

American (AMR) AF: 0.803 AC: 12275 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.914 AC: 3170 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4044 AN: 5142

South Asian (SAS) AF: 0.824 AC: 3975 AN: 4826

European-Finnish (FIN) AF: 0.712 AC: 7531 AN: 10572

Middle Eastern (MID) AF: 0.949 AC: 279 AN: 294

European-Non Finnish (NFE) AF: 0.803 AC: 54555 AN: 67974

Other (OTH) AF: 0.843 AC: 1784 AN: 2116

Alfa AF: 0.820 Hom.: 143833

Bravo AF: 0.838

Asia WGS AF: 0.770 AC: 2679 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.2
DANN	Benign	0.30
PhyloP100		-0.077

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4771996; hg19: chr13-98053792;